SummaryClusters
JL
7/19/2018
LSR vs FORTESSA
- ordered by machine, using only LSR for remaining
LSR vs FORTESSA
- ordered by machine, using only LSR for remaining
Raw centroids
- median value of markers in each cluster
Normalized centroids
- median z-score of markers in each cluster
Freq cluster
- median z-score of markers in each cluster
Freq population
- median z-score of markers in each cluster
Meta Phenograph +Meta tsne
## Running PhenoGraph... Finding nearest neighbors...DONE ~ 0.17 s
## Compute jaccard coefficient between nearest-neighbor sets...DONE ~ 1.872 s
## Build undirected graph from the weighted links...DONE ~ 0.354 s
## Run louvain clustering on the graph ...DONE ~ 0.195 s
## Return a community class
## -Modularity value: 0.8950466
## -Number of clusters: 23 DONE!## Running t-SNE...with seed 42 DONE- colored by “meta” phenograph cluster
Meta Phenograph +Meta tsne
- colored by control
Meta Phenograph +Meta tsne
- colored by percent of cells that are naive in original clusters
Meta Phenograph +Meta tsne
- colored by percent of cells that are effector in original clusters
Meta Phenograph +Meta tsne
- colored by percent of cells that are effector memory in original clusters
Meta Phenograph +Meta tsne
- colored by percent of cells that are central memory in original clusters
Meta Phenograph +Meta tsne
- colored by median CD45 (scaled) expression in original clusters
Meta Phenograph +Meta tsne
- colored by median CCR7 (scaled) expression in original clusters
Meta Phenograph +Meta tsne
- colored by median CD28 (scaled) expression in original clusters
Meta Phenograph +Meta tsne
- colored by median CD95 (scaled) expression in original clusters
Meta Phenograph +Meta tsne
- colored by median CD27 (scaled) expression in original clusters
Meta Phenograph +Meta tsne
- colored by median IgD (scaled) expression in original clusters
Meta Phenograph +Meta tsne
- colored by median CD19 (scaled) expression in original clusters
Meta Phenograph +Meta tsne
- meta-clusters 9, 2, 1, 16, 8
Meta Phenograph +Meta tsne
- meta-clusters 9, 2, 1, 16, 8
Meta Phenograph +Meta tsne
NOTES
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729477/
The total T cells (CD3+), helper T cells (CD3+CD4+), and total B cells (CD19+) were gated. The expression of mIgD on T and B cells was analyzed by calculating the percentages of CD3+IgD+, CD3+CD4+IgD+, immature B cells (CD19+IgM+IgD-) and mature B cells (CD19+IgD+) on a flow cytometer (model FC 500; Beckman Coulter Ltd., USA)
NOTES
- IgD values ~ 100 not really positive
- see https://github.com/PankratzLab/auto-fcs/issues/64
- higher CD19 not too weird on LSR